Freshwater molluscs are key components of aquatic ecosystems, contributing to ecosystem functioning. However, their diversity in southern Tamil Nadu remains poorly studied, especially in lentic ecosystems. We surveyed 41 waterbodies across the Tenkasi, Tirunelveli and Thoothukudi districts of Tamil Nadu to document species composition and water quality variables. A total of 24 species belonging to 18 genera and 12 families were recorded, accounting for 11.2% of India’s freshwater malacofauna. Gastropods dominated the assemblage (83%) compared to bivalves (17%). Gabbia travancoria and Idiopoma dissimilis were the most widespread species, whereas Pettancyclus tenuis and Corbicula striatella were restricted to single sites. Sundarapandipuram tank exhibited the highest richness with nine species. Physicochemical analysis revealed variation in conductivity, nutrients, and dissolved oxygen across sites, and CCA indicated that conductivity and nutrient enrichment were the primary drivers of species composition, with dissolved oxygen playing a secondary role. The frequent occurrence of pollution–tolerant and medically important taxa in human–use waterbodies highlights both ecological and public health concerns. This study provides the first regional checklist and highlights the need for long–term monitoring, habitat conservation, and integrated eco–health studies on freshwater molluscs.